Agreed. Crossbows are good for getting close and unleashing a hail of bolts against the enemy, especially lightly armoured foes. They can then reform and take a charge. If you're sitting them at a distance and hoping they will have the same effect then you're wasting their strengths.
Likewise, if you hope your RBT will fill the same roll as crossbows then you'll be disappointed. They don't have enough shots to really cut down the big infantry blocks, so don't try. What they can do is to hit heavy cavalry where it hurts (str 4 Armour piercing will make a dent on most). Or monsters. Or eagles.
Sure your enemy could be directing his artillery/magic/cavalry units at them, but if he is then its often going to take a couple of turns to do so. Take advantage of his eagerness to kill your bolt throwers to get in his face. If he is firing at your bolt throwers then it means the rest of your army is advancing unmolested. If he sends his fast cavalry against them then these are your targets.
Sure, they will fall apart like a house of cards against melee scouts such as our dearly beloved shades, but that is a problem that all warmachines suffer.
Don't think about "are they worth it." Instead think "how can I MAKE them worth it"
In my 2500 list I'm taking 30 Crossbows and two Bolt Throwers. They will each have a role to serve. They may or may not make their points back, but that is a term I loathe and despise. I want them to keep the rest of my army safe by picking off or thinning out threats from long range. I have a Pegasus Master who can act as a swift moving anti-scout force. I can even deploy my own shades on my back field to protect my rear if I know my opponent has scouts himself.
Deployment wise, there are three viable options:
1) Stick them both behind your lines, ideally on a hill and preferably with cover. If your opponent wants them then he will have most of your army in the way to get to them. If he is hitting them at range with magic or artillery then he is not hitting the rest of your army.
2) Deploy both of them on a flank, a long way from your main force. If he chooses to divert resources into dealing with them then they have a long way to go, and it means that you have more turns to shoot them on their way and that his RBT Killers are a long way from the rest of the battle
3) Deploy one on each flank. Similar to option 2, but this time he would need to either send two hit teams to get rid of them, or he would have to spend a long time getting from one to the other. And they and the rest of your army are not going to sit idly by while they do so.
Of course, their two biggest weaknesses are magic and shooting. As such, determine how best to negate that threat. I don't know who you're fighting, so I can't state the best way of doing so, but if your artillery is weak then his is also.
Personally, I'm more than happy for my opponent to throw cannon balls against my bolt throwers if it means they aren't going against my Hydra. And if he has magic, then so do you. That's why the good lord gave us dispel dice.
I'm far from an expert on Bolt Throwers, but I enjoy the tactical challenges they represent. Using an overpriced/underpowered unit and getting the most from it will encourage you to think in new ways and make you a better general. It also gives the enemy something they might not have expected. Everyone facing Dark Elves expects to see a Hydra or two. They may not expect bolt throwers which can target his anti-hydra units - knights and cannons.
Apologies if any of that seems ranty. I seem to be determined to stick up for the poor much maligned Bolt Thrower crews who are sobbing into their dwarf-skin handkerchiefs.